Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/2C2_R1_001.fastp-trim.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/output/01.20-D-Apul-WGBS-trimming-fastp-FastQC-MultiQC/2C2_R2_001.fastp-trim.fq.gz (version: v0.24.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	42517358
Number of paired-end alignments with a unique best hit:	25641026
Mapping efficiency:	60.3% 
Sequence pairs with no alignments under any condition:	7511287
Sequence pairs did not map uniquely:	9365045
Sequence pairs which were discarded because genomic sequence could not be extracted:	25

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12837067	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	12803934	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1190692671

Total methylated C's in CpG context:	16520048
Total methylated C's in CHG context:	1299736
Total methylated C's in CHH context:	5158938
Total methylated C's in Unknown context:	62669

Total unmethylated C's in CpG context:	178408348
Total unmethylated C's in CHG context:	204738708
Total unmethylated C's in CHH context:	784566893
Total unmethylated C's in Unknown context:	2919423

C methylated in CpG context:	8.5%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.7%
C methylated in unknown context (CN or CHN):	2.1%


Bismark completed in 0d 2h 49m 43s